Biology subjects

Du, Y.

Publications and source records attributed to Du, Y..

At least 271 records · Page 15Linked to original sources

bioRxiv2020

Lung at a Glance: an integrative web toolset of lung ontology, imaging and single cell omics

Recent advances in single-cell omics and high-resolution imaging have provided unanticipated data resources for the elucidation of genes underlying the complex biological processes critical for organ formation and function. However, processing and integrating large amounts of single-cell omics and imaging data presents a major challenge for most researchers. There is a critical need for ready-to-use computational tools for data/knowledge integration and visualization. Here we present "Lung-at-a-glance", an easy-to-use web toolset for visualizing and interoperating complex omics and imaging data, providing an interactive web interface to bridge lung anatomic ontology classifications to lung histology and immunofluorescence confocal images, and cell-type-specific gene expression. "Lung-at-a-glance" contains three interactive components: 1) "Region at a glance", 2) "Cell at a glance" and 3) "Gene at a glance". "Lung-at-a-glance" and other newly developed web tools for lung-related data query, integration and visualization are publicly available on LGEA web portal v3 https://research.cchmc.org/pbge/lunggens/mainportal.html.

bioinformatics↗

bioRxiv2020

Post-mitotic myotubes repurpose the cytokinesis machinery to effect cellular guidance

Embryogenesis depends on a tightly regulated balance between mitosis, differentiation, and morphogenesis. Understanding how the embryo uses a relatively small number of proteins to transition between growth and morphogenesis is a central question of developmental biology, but the mechanisms controlling mitosis and differentiation are considered to be fundamentally distinct. Here we show the mitotic kinase Polo, which regulates all steps of mitosis [1-3], also directs cellular morphogenesis after cell cycle exit. In mitotic cells, the Aurora kinases activate Polo to control a cytoskeletal regulatory module that directs cytokinesis [4-6]. We show that in the post-mitotic mesoderm, the control of Polo activity transitions from the Aurora kinases to the uncharacterized kinase Back Seat Driver (Bsd), where Bsd and Polo cooperate to regulate muscle morphogenesis. Polo and its effectors therefore direct mitosis and cellular morphogenesis, but the transition from growth to morphogenesis is determined by the spatiotemporal expression of upstream activating kinases.

cell biology↗

bioRxiv2020

The utility of native MS for understanding the mechanism of action of repurposed therapeutics in COVID-19: heparin as a disruptor of the SARS-CoV-2 interaction with its host cell receptor.

The emergence and rapid proliferation of the novel coronavirus (SARS-CoV-2) resulted in a global pandemic, with over six million cases and nearly four hundred thousand deaths reported world-wide by the end of May 2020. A rush to find the cures prompted re-evaluation of a range of existing therapeutics vis-a-vis their potential role in treating COVID-19, placing a premium on analytical tools capable of supporting such efforts. Native mass spectrometry (MS) has long been a tool of choice in supporting the mechanistic studies of drug/therapeutic target interactions, but its applications remain limited in the cases that involve systems with a high level of structural heterogeneity. Both SARS-CoV-2 spike protein (S-protein), a critical element of the viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively glycosylated, making them challenging targets for native MS. However, supplementing native MS with a gas-phase ion manipulation technique (limited charge reduction) allows meaningful information to be obtained on the non-covalent complexes formed by ACE2 and the receptor-binding domain (RBD) of the S-protein. Using this technique in combination with molecular modeling also allows the role of heparin in destabilizing the ACE2/RBD association to be studied, providing critical information for understanding the molecular mechanism of its interference with the virus docking to the host cell receptor. Both short (pentasaccharide) and relatively long (eicosasaccharide) heparin oligomers form 1:1 complexes with RBD, indicating the presence of a single binding site. This association alters the protein conformation (to maximize the contiguous patch of the positive charge on the RBD surface), resulting in a notable decrease of its ability to associate with ACE2. The destabilizing effect of heparin is more pronounced in the case of the longer chains due to the electrostatic repulsion between the low-pI ACE2 and the heparin segments not accommodated on the RBD surface. In addition to providing important mechanistic information on attenuation of the ACE2/RBD association by heparin, the study demonstrates the yet untapped potential of native MS coupled to gas-phase ion chemistry as a means of facilitating rational repurposing of the existing medicines for treating COVID-19. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/142794v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@ce764corg.highwire.dtl.DTLVardef@b8909corg.highwire.dtl.DTLVardef@11e13fcorg.highwire.dtl.DTLVardef@1b2383a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Mechanistic insights into ventricular arrhythmogenesis of hydroxychloroquine and azithromycin for the treatment of COVID-19

Background: Recent reports on the use of hydroxychloroquine (HCQ) alone, or combined with azithromycin (AZM) in the management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have raised cardiac safety concerns. Currently, there is limited mechanistic data evaluating cardiac safety with HCQ and AZM therapy. Methods: Using comprehensive In Vitro ProArrhythmia Assay (CiPA) Schema IC50 paradigms, we examined the cardiac electrophysiological effects of HCQ and HCQ/AZM. Molecular modelling explored HCQ and AZM binding properties to hERG. Langendorff-perfused guinea-pig hearts were electrically and optically mapped by multi-electrode array and voltage (RH237) and Ca2+ (Rhod-2 AM) dyes. Human action potential and ion current reconstructions were performed in silico. Results: HCQ blocked IKr and IK1 with IC50 concentrations (10+-0.6 and 34+-5.0 microM) within the therapeutic range observed clinically. HCQ also blocked INa and ICaL but at higher IC50, whilst Ito and IKs were unaffected. Contrastingly, AZM produced minor inhibition of INa, ICaL, IKs, and IKr,, with no effect on IK1 and Ito. HCQ + AZM combined inhibited IKr and IK1 with IC50s of 7.7 +- 0.8 microM and 30.4 +- 3.0 microM, but spared INa, ICaL and Ito,. Molecular modelling confirmed potential HCQ binding to hERG. Cardiac mapping and ECG studies in isolated hearts demonstrated that HCQ slowed heart rate and ventricular conduction with associated prolongation of PR, QRS and QT intervals. Optical mapping demonstrated, and prolonged, more heterogeneous, action potential durations and intracellular Ca2+ transients. These effects were accentuated with combined HCQ+AZM treatment, which elicited electrical alternans, re-entrant circuits and wave breaks. Reconstruction in a human in-silico model demonstrated that this is attributable to the integrated action of HCQ and AZM reducing IKr, IKs and IK1. Conclusions: These data provide an electrophysiological basis for recent FDA guidelines cautioning against combined HCQ/AZM administration for the treatment of Covid-19 on the grounds of potential cardiac safety. We would strongly recommend monitoring of electrocardiographic QT interval with the use of this combination of medications.Competing Interest StatementThe authors have declared no competing interest.

pharmacology and toxicology↗

bioRxiv2020

Auranofin resistance in Toxoplasma gondii decreases the accumulation of reactive oxygen species but does not target parasite thioredoxin reductase

Auranofin, a reprofiled FDA-approved drug originally designed to treat rheumatoid arthritis, has emerged as a promising anti-parasitic drug. It induces the accumulation of reactive oxygen species (ROS) in parasites, including Toxoplasma gondii. We generated auranofin resistant T. gondii lines through chemical mutagenesis in order to identify the molecular target of this drug. Resistant clones were confirmed with a competition assay using wild-type T. gondii expressing yellow fluorescence protein (YFP) as a reference strain. The predicted auranofin target, thioredoxin reductase, was not mutated in any of our resistant lines. Subsequent whole genomic sequencing analysis (WGS) did not reveal a consensus resistance locus, although many have point mutations in genes encoding redox-relevant proteins such as superoxide dismutase (TgSOD2) and ribonucleotide reductase. We investigated the SOD2 L201P mutation and found that it was not sufficient to confer resistance when introduced into wild-type parasites. Resistant clones accumulated less ROS than their wild type counterparts. Our results demonstrate that resistance to auranofin in T. gondii enhances its ability to abate oxidative stress through diverse mechanisms. This evidence supports a hypothesized mechanism of auranofin anti-parasitic activity as disruption of redox homeostasis.

microbiology↗

bioRxiv2020

Hype versus hope: Deep learning encodes more predictive and robust brain imaging representations than standard machine learning

Previous successes of deep learning (DL) approaches on several complex tasks have hugely inflated expectations of their power to learn subtle properties of complex brain imaging data, and scale to large datasets. Perhaps as a reaction to this inflation, recent critical commentaries unfavorably compare DL with standard machine learning (SML) approaches for the analysis of brain imaging data. Yet, their conclusions are based on pre-engineered features which deprives DL of its main advantage: representation learning. Here we evaluate this and show the importance of representation learning for DL performance on brain imaging data. We report our findings from a large-scale systematic comparison of SML approaches versus DL profiled in a ten-way age and gender-based classification task on 12,314 structural MRI images. Results show that DL methods, if implemented and trained following the prevalent DL practices, have the potential to substantially improve compared to SML approaches. We also show that DL approaches scale particularly well presenting a lower asymptotic complexity in relative computational time, despite being more complex. Our analysis reveals that the performance improvement saturates as the training sample size grows, but shows significantly higher performance throughout. We also show evidence that the superior performance of DL is primarily due to the excellent representation learning capabilities and that SML methods can perform equally well when operating on representations produced by the trained DL models. Finally, we demonstrate that DL embeddings span a comprehensible projection spectrum and that DL consistently localizes discriminative brain biomarkers, providing an example of the robustness of prediction relevance estimates. Our findings highlight the presence of non-linearities in brain imaging data that DL frameworks can exploit to generate superior predictive representations for characterizing the human brain, even with currently available data sizes.

neuroscience↗

bioRxiv2020

Expression from DIF1-motif promoters of hetR and patS is dependent on HetZ and modulated by PatU3 during heterocyst differentiation

HetR and PatS/PatX-derived peptides are the activator and diffusible inhibitor for cell differentiation and patterning in heterocyst-forming cyanobacteria. HetR regulates target genes via HetR-recognition sites. However, some genes (such as patS/patX) upregulated at the early stage of heterocyst differentiation possess DIF1 (or DIF+) motif (TCCGGA) promoters rather than HetR-recognition sites; hetR possesses both regulatory elements. How HetR controls heterocyst-specific expression from DIF1 motif promoters remains to be answered. This study presents evidence that the expression from DIF1 motif promoters of hetR, patS and patX is more directly dependent on hetZ, a gene regulated by HetR. The HetR-binding site upstream of hetR is not required for its autoregulation. PatU3 (3 portion of PatU) that interacts with HetZ may modulate HetZ-dependent gene expression. These findings contribute to understanding of the mutual regulation of hetR, hetZ-patU and patS/patX in a large group of multicellular cyanobacteria.

microbiology↗

bioRxiv2020

Comprehensive transcriptome data of normal and Ascosphaera apis-infected western honeybee larval guts

ABSTRAmTApis mellifera ligustica is a well-known subspecies of western honeybee, Apis mellifera. Ascosphaera apis is a common fungal pathogen of honeybee larvae, resulting in Chalkbrood disease. In this article, deep sequencing of un-treated 4-, 5-, and 6-day-old larval guts (AmCK1, AmCK2, AmCK3) and A. apis-treated 4-, 5- and 6-day-old larval guts (AmT1, AmT2, AmT3) of Apis mellifera ligustica were conducted using Illumina HiSeq 4000 platform. In total, 85811046, 81962296, 85636572, 79267686, 82889882, and 100211796 raw reads were respectively yielded from above-mentioned six groups. The result of sequencing satuation analysis suggested that the sequencing depth in this work was enough to detect nearly all expressed genes. After quality control, 85739414, 81896402, 85573798, 79202304, 82828926, and 100128692 clean reads were obtained. Additionally, the GC content of each group was above 45.26%. Furthermore, 47035852, 65612676, 71803878, 62560904, 65018360, and 56278272 clean reads were mapped to the Apis mellifera genome, including 41221479, 61172916, 66724233, 57531335, 60245732, and 52638986 unique mapped clean reads, and 2078427, 986825, 915375, 1082925, 1097130, and 716436 multiple mapped clean reads. In addition, exons were the most abundant regions mapped by clean reads, follow by intergenic regions and introns. The strand-specific cDNA library-based RNA sequencing data documented here will faciliate study on molecualr mechanisms underlying host immune response and host-pathogen interaction during chalkbrood disease, and benefit understanding of non-coding RNA-mediated cross-kingdom regulation between A. m. ligustica larvae and A. apis. Value of the DataO_LIThis data reported here could be used to explore circRNAs, lncRNAs, mRNAs and their competing endogenous RNA networks involved in response of western honeybee larvae to Ascosphaera apis infection. C_LIO_LIThe current data contributes to better understanding mechanisms regulating host-pathogen interaction during chalkbrood disease. C_LIO_LIOur data can provide novel insights into understanding non-coding RNA-mediated cross-kingdom regulation between Apis mellifera ligustica and A. apis. C_LI

molecular biology↗

bioRxiv2020

Isoform-specific regulation of HCN4 channels by a family of endoplasmic reticulum proteins

Ion channels in excitable cells function in macromolecular complexes in which auxiliary proteins modulate the biophysical properties of the pore-forming subunits. Hyperpolarization-activated, cyclic nucleotide-sensitive HCN4 channels are critical determinants of membrane excitability in cells throughout the body, including thalamocortical neurons and cardiac pacemaker cells. We previously showed that the properties of HCN4 channels differ dramatically in different cell types, possibly due to the endogenous expression of auxiliary proteins. Here, we report the discovery of a family of endoplasmic reticulum transmembrane proteins that interact with and modulate HCN4. Lymphoid-restricted membrane protein (LRMP, Jaw1) and inositol trisphosphate receptor-associated guanylate kinase substrate (IRAG, Mrvi1, Jaw1L) are homologous proteins with small ER luminal domains and large cytoplasmic domains. Despite their homology, LRMP and IRAG have distinct effects on HCN4. LRMP is a loss-of-function modulator that inhibits the canonical depolarizing shift in the voltage-dependence of HCN4 activation in response to binding of cAMP. In contrast, IRAG causes a gain of HCN4 function by depolarizing the basal voltage-dependence of activation in the absence of cAMP. The mechanisms of action of LRMP and IRAG are novel; they are independent of trafficking and cAMP binding, and they are specific to the HCN4 isoform. We also found that IRAG is highly expressed in the mouse sinoatrial node where computer modeling predicts that its presence increases HCN4 availability. Our results suggest important roles for LRMP and IRAG in regulation of cellular excitability and as tools for advancing mechanistic understanding of HCN4 channel function. Significance statementThe pore-forming subunits of ion channels are regulated by auxiliary interacting proteins. Hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channels are critical determinants of electrical excitability in many types of cells including neurons and cardiac pacemaker cells. Here we report the discovery of two novel HCN4 regulatory proteins. Despite their homology, the two proteins -- lymphoid-restricted membrane protein (LRMP) and inositol trisphosphate receptor-associated guanylate kinase substrate (IRAG) -- have opposing effects on HCN4, causing loss- and gain-of-function, respectively. LRMP and IRAG are expected to play critical roles in regulation of physiological processes ranging from wakefulness to heart rate through their modulation of HCN4 channel function.

physiology↗

bioRxiv2020

Pacific Biosciences long reads-based genome sequencing data from a widespread bee fungal parasite, Nosema ceranae

Nosema ceranae is a widespread fungal parasite that infects both adult honeybee and honeybee larvae, leading to microsporidiosis, which seriously affects bee health and apicultural industry. In this article, genome sequencing of clean spores of N. ceranae was conducted using third-generation Pacific Biosciences (PacBio) single molecule real time (SMRT) sequencing technology. In total, 152671 subreads were obtained after quality control of raw reads from PacBio SMRT sequencing, with a N50 and average length of 14422 bp and 11310 bp, respectively. Additionally, the length distribution of subreads was from 10000 bp to more than 50000 bp. Nineteen scaffords with a total length of 7354221 bp were assembled, and the N50, N90 and maximum scafford length were 728543 bp, 198795 bp and 1917792 bp, respectively. The GC content was 25.97%. Furthermore, by integration of genes predicted from de novo and homology-based methods, 3112 N. ceranae genes were finally assembled, with a total length of 2730179 bp and mean length of 877.31 bp. In addition, the total length and mean length of exons were 2657637 bp and 854 bp, respectively; and the total length and mean length of introns were 72542 bp and 23.31 bp, respectively. The genome sequencing data documented here will give deep insights into the molecular biology of N. ceranae, facilitate exploration of genes and pathways associated with toxin factors and infection-related factors, and benefit research on comparative genomics and phylogenetic diversity of Nosema species.

bioinformatics↗

bioRxiv2020

Genome-wide bisulfite sequencing data of normal and Ascosphaera apis-infected larval guts of eastern honeybee

Apis cerana cerana, a subspecies of eastern honey, Apis cerana, plays a specific role in beekeeping industry and ecosystem in China and other Asian countries. Larvae of A. c. cerana can be infected by Ascosphaera apis, the fungal pathogen of chalkbrood. In this article, normal 4-, 5-, and 6-day-old larval guts (AcCK1, AcCK2, AcCK3) and A. apis-infected 4-, 5- and 6-day-old larval guts (AcT1, AcT2, AcT3) of A. c. cerana workers were respectively harvested followed by DNA isolation, bisulfite conversion, cDNA library construction and Illumina sequencing. Based on genome-wide bisulfite sequencing, 79167210, 82175052, 79331489, 81051009, 74742842 and 74849091 raw reads were generated from AcCK1, AcCK2, AcCK3, AcT1, AcT2 and AcT3, and after quality control, 73417030 (92.73%), 76660370 (93.27%), 71804727 (90.44%), 75046507 (92.82%), 67487782 (90.30%) and 67367023 (90.04%) clean reads were obtained, respectively. Additionally, 73333333, 76533333, 71466667, 75066667, 67590965 and 67200000 clean reads were mapped to the reference genome of A. cerana, including 54656767, 58583415, 54127407, 57943220, 52547867 and 51295824 unique mapped clean reads, and 8624392, 8789458, 7531333, 7747337, 6249679 and 5394174 multiple mapped clean reads. The genome-wide bisulfite sequencing data reported here can be used for genome-wide identification of 5mC methylation sites in eastern honeybee larval guts and systematic investigation of DNA methylation-mediated host response to A. apis infection. Value of the dataO_LIThe current dataset contributes to genome-wide identification of 5mC methylation sites in normal and A. apis-infected larval guts of eastern honeybee. C_LIO_LIThe reported data could be used for systematic investigation of DNA methylation-mediated response of eastern honeybee larvae to A. apis infection. C_LIO_LIOur data offers a valuable genetic resource for better understanding epigenetic regulation mechanism involved in eastern honeybee larvae-A. apis interaction. C_LI

molecular biology↗

bioRxiv2020

Whole genome bisulfite sequencing dataset of mycelium and spore of chalkbrood disease pathogen Ascosphaera apis

Chalkbrood, a widespread fungal disease of bee larvae, is caused by the fungus Ascosphaera apis. In this article, mecylia and spores of A. apis were respectively collected followed by DNA isolation, bisulfite conversion, cDNA library construction and next-generation sequencing. Using whole genome bisulfite sequencing (WGBS), 69,844,360 and 60,570,990 raw reads were yielded from Aam and Aas, and after quality control, 9,982,386,951 and 8,825,601,434 clean reads were obtained, respectively. In addition, 67,685,866 and 58,886,072 clean reads were mapped to the reference genome of A. apis, including 37,643,592 and 31,568,442 unique mapped clean reads, and 49,686 and 13,348 multiple mapped clean reads. Furthermore, after bisulfite treatment, the conversion ratio of clean reads from Aam and Aas were 99.38% and 99.51%, respectively. The WGBS data ducumented here contributes to genome-wide identification of 5mC methylation sites in A. apis and comparison of methylomes between mycelium and spore. Value of the dataO_LIThis dataset can be used for genome-wide identification of 5mC methylation sites in A. apis. C_LIO_LIThe accessible data could be used to systematically compare methylomes between mycelium and spore of A. apis. C_LIO_LICurrent data provides a useful resource for further study on DNA methylation-mediated mechanism underlying mycelium growth, spore germination and sexual reproduction of mycelium with the opposite sex. C_LI

molecular biology↗

bioRxiv2020

Nanopore-based long-read transcriptome data of Nosema ceranae-infected and un-infected western honeybee workers' midguts

Apis mellifera ligustica is a subspecies of western honeybee, Apis mellifera. Nosema ceranae is known to cause bee microspodiosis, which seriously affects bee survival and colony productivity. In this article, Nanopore long-read sequencing was used to sequence N. ceranae-infected and un-infected midguts of A. m. ligustica workers at 7 d and 10 d post inoculation (dpi). In total, 5942745, 6664923, 7100161 and 6506665 raw reads were respectively yielded from AmT1, AmT2, AmCK1 and AmCK2, with average lengths of 1148, 1196, 1178 and 1201 bp, and N50 of 1328, 1394, 1347 and 1388 bp. The length distribution of raw reads from AmT1, AmT2, AmCK1 and AmCK2 was ranged from 1 kb to more than 10 kb. Additionally, the distribution of quality score of raw reads from AmT1 and AmT2 was among Q6[~]Q12, while that from AmCK1 and AmCK2 was among Q6[~]Q16. Further, 5745048, 6416987, 6928170, 6353066 clean reads were respectively gained from AmT1, AmT2, AmCK1 and AmCK2, and among them 4172542, 4638289, 5068270 and 4857960 were identified as being full-length. After removing redundant reads, the length distribution of remaining full-length transcripts was among 1 kb[~]8 kb, with the most abundant length of 2 kb. The long-read transcriptome data reported here contributes to a deeper understanding of the molecular regulating N. ceranae-response of A. m. ligustica and host-fungal parasite interaction during microsporidiosis.

bioinformatics↗

bioRxiv2020

A full-length transcriptome dataset of normal and Nosema ceranae-challenged midgut tissues of eastern honeybee workers

Apis cerana cerana is a subspecies of eastern honeybee, Apis cerana, and it plays a vital role in ecological maintenance in China. However, A. c. cerana is threatened by many pathogenic microorganisms including Nosema ceranae, a widespread fungal parasite that infected worldwide colonies. In this article, un-challenged (AcCK1, AcCK2) and N. ceranae-challenged midguts of A. c. cerana workers (AcT1, AcT2) were sequenced utilizing Nanopore long-read sequencing technology. Totally, 11,727,628, 6,996,395, 14,383,735 and 11,580,154 raw reads were yielded from AcCK1, AcCK2, AcT1 and AcT2; the average lengths were 1147 bp, 908 bp, 992 bp and 1077 bp, and the average N50 were 1308 bp, 911 bp, 1079 bp and 1192 bp. The length distribution of was ranged 1 kb to more than 10 kb. Additionally, the quality (Q) score distribution of raw reads was among Q7~Q17. Further, 11,617,144, 6,940,895, 14,277,240 and 11,501,562 clean reads were respectively obtained from AcCK1, AcCK2, AcT1 and AcT2, and among them 78.40%, 82.50%, 79.05% and 80.20% were identified as full-length clean reads. In addition, full-length clean reads from AcCK1, AcT1, AcT2 and AcCK2 were ranged from 1 kb to more than 10 kb in length. Finally, the length distribution of redundant reads-removed full-length transcripts was among 1 kb~5 kb. Value of the data{diamondsuit} This dataset enables better understanding the complexity of A. c. cerana transcriptome. {diamondsuit}Current dataset contributes to identification of genes and transcripts engaged in response of eastern honeybee to N. ceranae stress. {diamondsuit}The data provides a valuable genetic resource for deciphering alternative splicing and polyadenylation of A. c. cerana mRNAs involved in host response to N. ceranae challenge. {diamondsuit}The reported data is beneficial for uncovering the molecular mechanism regulating interaction between eastern honeybee and microsporidian.

molecular biology↗

bioRxiv2020

PacBio SMRT-based full-length transcriptome data of Ascosphaera apis mycelium and spore

Ascosphaera apis is an entomopathogenic fungus that exclusively infects honeybee larvae, resulting in chalkbrood disease, a widespread fungal disease damaging the beekeeping industry all over the world. In this article, purified mycelia (Aam) and spores (Aas) of A. apis pure culture under lab condition were sequenced using PacBio Sequel platform. In total, 13,302,489 and 9,911,345 subreads were yielded from Aam and Aas, respectively; 394,142 and 274,928 circular consensus sequence (CCS) reads were identified as being full-length non-chimeric (FLNC) reads, with a mean length of 2820 bp and 2602 bp, respectively. Furthermore, 174,095 and 103,845 corrected isoforms were identified, with a N50 length of 3543 bp and 3262 bp, respectively. The reported full-length transcriptome data of A. apis mycelium and spore will provide a valuable resource for improvement of genome and transcriptome annotations as well as better understanding of transcript structure such as alternative splicing and polyadenylation. Value of the dataO_LICurrent dataset offers a set of high-quality full-length transcripts of A. apis. C_LIO_LIThe data can facilitate the improvement of A. apis genome and transcriptome annotations. C_LIO_LIThis dataset benefits further exploration of alternative splicing and polyadenylation of A. apis mRNAs. C_LI

evolutionary biology↗

bioRxiv2020

MeRIP-seq and RNA-seq data of mycelium and spore of Ascosphaera apis, a widespread bee fungal pathogen

Ascosphaera apis is widespread fungal pathogen of honeybee larvae, causing chalkbrood, a chronic disease that weakens bee health and colony productivity. In this article, mecylia and spores of A. apis were respectively purified followed by RNA isolation, cDNA library construction, MeRIP-seq and RNA-seq. A total of 62,551,172, 41,773,158, 49,535,092 and 61,569,610 raw reads were produced from Aam_IP, Aas_IP, Aam_input and Aas_input groups, respectively. After quality control, 58,484,368, 37,381,432, 44,655,434 and 58,739,742 clean reads were obtained. Furthermore, 47,706,205, 31,356,690, 35,259,810 and 44,319,061 clean reads were mapped to the reference genome of A. apis, including 39,337,036, 26,731,957, 31,987,396 and 40,017,855 unique mapped reads, and 8,369,169, 4,624,733, 3,272,414 and 4,301,206 multiple mapped reads. Among them, 96.31%, 96.51%, 96.82% and 97.11% of clean reads were mapped to exons; 2.09%, 2.31%,1.83% and 1.81% to introns; 1.60%, 1.18%, 1.35% and 1.08% to intergenic regions. Value of the dataO_LIThe data can be used to investigate the relationship between the m6A modification extent and the transcript level in the A. apis transcriptome. C_LIO_LIThis dataset contributes to transcriptome-wide characterization of the m6A distributing patterns in mRNAs and non-coding RNAs in A. apis mycelium and spore. C_LIO_LICurrent data benefits new functions of m6A modification in the transcripts extensively modified by m6A in A. apis mycelium and spore. C_LIO_LIOur data could be used to characterize differential patterns of the m6A methylation between mycelium and spore of A. apis. C_LI

molecular biology↗

bioRxiv2020

Whole transcriptome data of uninfected and Nosema ceranae-infected midguts of eastern honeybee workers

Apis cerana cerana is a subspecies of eastern honeybee, Apis cerana. Nosema ceranae is a widespread fungal parasite of honeybee, causing heavy losses for beekeeping industry all over the world. In this article, total RNA of normal midguts (AcCK1, AcCK2) and N. ceranae-infected midguts of A. c. cerana workers at 7 d and 10 d post inoculation (AcT1, AcT2) were respectively isolated followed by strand-specific cDNA library construction and next-generation RNA sequencing. In tolal, 56270223688, 44860946964, 78991623806, and 92712308296 raw reads were derived from AcCK1, AcCK2, AcT1 and AcT2, respectively. Following strict quality control, 54495191388, 43570608753, 76708161525, and 89467858351 clean reads were obtained, with Q30 value of 95.80%, 95.99%, 96.07% and 96.04%, and GC content of 44.20%, 43.44%, 44.83% and 43.63%, respectively. The raw data were submitted to the NCBI Sequence Read Archive database and connected to BioProject PRJNA562784. These data offers a valuable resource for deep investigation of mechanisms underlying eastern honeybee responding to N. ceranae infection and host-fungal parasite interaction during microsporidiosis. Value of the DataO_LICurrent dataset offers a valuable resource for exploring mRNAs, lncRNAs and circRNAs involved in response of A. c. cerana worker to N. ceranae infection. C_LIO_LIThe accessible data can be used to investigate differential expression pattern and regulatory network of non-coding RNAs in A. c. cerana workers midguts responding to N. ceranae challenge. C_LIO_LIThis data will enable a better understanding of the molecular mechanism regulating eastern honeybee-N. ceranae interaction. C_LI

bioinformatics↗

bioRxiv2020

Nanopore long-read transcriptome data of fungal pathogen of chalkbrood disease, Ascosphaera apis

Ascosphaera apis is a fungal pathogen that exclusively infects honeybee larvae, leading to chalkbrood disease, which damages the number of adult honeybees and colony productivity. In this article, A. apis mecylia and spores were respectively purified followed by Oxford Nanopore sequencing via PromethION platform. In total, 6,321,704 and 6,259,727 raw reads were generated from Aam and Aas, with a length distribution among 1 kb~10 kb. The quality (Q) scores of majority of raw reads were Q9 (Aam) and Q11 (Aas). Additionally, 5,669,436 and 6,233,159 clean reads were gained, among them 79.32% and 79.62% were identified as being full-length. The lengths of redundant reads-removed full-length transcripts were among 1 kb~8 kb and 1 kb~9 kb, and most abundant length for both was 1 kb. Furthermore, the length of redundant transcripts-removed clean reads was ranged from 1 kb~7 kb, with the largest group of 1 kb. The data reported here provides a beneficial genetic resource for improving genome and transcriptome annotations of A. apis and for exploring alternative splicing and polyadenylation of A. apis mRNAs. Value of the resultO_LICurrent dataset enables better understanding of the complexity of A. apis transcriptome. C_LIO_LIThe long-read transcriptome data can be used to identify of genes and transcripts associated with A. apis infection mechanism. C_LIO_LIThe accessible data provides full-length transcripts for improving gene structure and functional annotation of A. apis transcriptome. C_LIO_LIThis dataset could be utilized for investigation of alternative splicing and polyadenylation of A. apis mRNAs. C_LI

molecular biology↗